I'll leave it to you to turn it back into a one-liner:

use POSIX 'mktime';
while(<DATA>){
        if(/^((\d{4})-(\d{2})-(\d{2})\s(\d{2}):(\d{2}):(\d{2}),(\d{3})
+)/){ 
                $t2=mktime($7,$6,$5,$4-1,$3-1,$2-1900,0,0,0)*1000+$8-$
+t; 
                if($t){print "$1 $t2\n";$t=0}else{$t=$t2}
        }
}

__DATA__
2010-11-04 11:20:04,101
2010-11-04 11:23:10,110
2010-11-05 11:20:04,101
2010-11-05 11:23:10,102
[download]

And I am not saying it is a better way to write this. Just shorter.